Phylo cookbook

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* Distance matrix: cells are branch lengths if a branch exists, otherwise Inf or NaN
 
* Distance matrix: cells are branch lengths if a branch exists, otherwise Inf or NaN
 
* Relationship matrix? See [http://www.jstor.org/stable/3070822 Martins and Housworth 2002]
 
* Relationship matrix? See [http://www.jstor.org/stable/3070822 Martins and Housworth 2002]
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[[Category:Cookbook]]

Revision as of 16:01, 25 June 2010

Here are some examples of using Bio.Phylo for some likely tasks. Some of the given functions might be added to Biopython in a later release, but you can use them in your own code with Biopython 1.54.

Contents

Consensus methods

TODO:

  • Majority-rules consensus


Rooting methods

TODO:

  • Root at the midpoint between the two most distant nodes (or "center" of all tips)
  • Root with the given outgroup (terminal or nonterminal)


Exporting to other types

Convert to a PyCogent tree

The tree objects used by Biopython and PyCogent are different. Nonetheless, both toolkits support the Newick file format, so interoperability is straightforward at that level:

from Bio import Phylo
import cogent
 
Phylo.write(bptree, 'mytree.nwk', 'newick')  # Biopython tree
ctree = cogent.LoadTree('mytree.nwk')        # PyCogent tree

TODO:

  • Convert objects directly, preserving some PhyloXML annotations if possible


Convert to a NumPy array or matrix

TODO:

  • Adjacency matrix: cells are True if parent-child relationship exists, otherwise False
  • Distance matrix: cells are branch lengths if a branch exists, otherwise Inf or NaN
  • Relationship matrix? See Martins and Housworth 2002
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